I'm currently a research fellow working on the PRESTA project, which aims to identify a core stress-response network in the model organism Arabidopsis thaliana using systems biology. My research includes developing methods for analysing genome scale time series data, including network inference algorithms that can learn from multiple (time-series) datasets.

RESEARCH INTERESTS

My current interest lies in Systems Biology and includes:

• Systems biology approaches to identifying stress-related genes. Currently identifying gene regulatory networks common over several stress in Arabidopsis thaliana, in order to allow for more targeted interventions and manipulation for purpose.
• More generally, I'm interested in using systems biology approches for targeted interventions in crops for global food security issues, and for identifying organisms responses to exotic environments e.g., hypo/hyper-gravity.

Chromosome Behaviour

• Realistic models of chromosome behaviour using polymer statistics. Previous work in this area has focussed on using MCMC methods to sample chromosome trajectories when centromeres/telomeres are tethered to the nuclear periphery and directionally biased, capturing the organisation of chromosomes during meiosis (Rabl and the Bouquet).
• Future models will include additional attractive fields between homologues (or sub-regions of homologues), representing the influence of chromosome pairing and/or recombination.

SOFTWARE

PUBLICATIONS

• Nonparametric Bayesian Inference for Perturbed and Orthologous Gene Regulatory Networks. 2012. C.A. Penfold, V. Buchanan-Wollaston, K.J. Denby and D.L. Wild. Bioinformatics (In press).
• Modeling Meiotic Chromosomes Indicates a Size Dependent Contribution of Telomere Clustering and Chromosome Rigidity to Homologue Juxtaposition. 2012. C.A. Penfold, P.E. Brown, N.D. Lawrence and A.S. H. Goldman. PLoS Comput Biol 8(5): e1002496. doi:10.1371/journal.pcbi.1002496
• How to infer gene networks from expression profiles, revisited. 2011. C.A. Penfold and D.L. Wild. Interface Focus 1(1) 857-870. doi: 10.1098/rsfs.2011.0058
• High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation. 2011. E. Breeze, E. Harrison, S. McHattie, L. Hughes, R. Hickman, C. Hill, S. Kiddle, Y.S. Kim, C.A. Penfold, D. Jenkins, C. Zhang, K. Morris, C. Jenner, S. Jackson, B. Thomas, A. Tabrett, R. Legaie, J.D. Moore, D.L. Wild, S. Ott, D. Rand, J. Beynon, K. Denby, A. Mead, V. Buchanan-Wollaston. The Plant Cell 23(3):873-94. doi: 10.1105/tpc.111.083345